That may solve a lot of your problems.
Try doing the conversion to small JPEG manually, too, and see if that produces different results. It's not hard:
1. use Image / Image Size to reduce the size of the image - try setting the longer dimension to 600 pixels (the shorter dimension should scale to maintain the aspect ratio). I often change the dpi here, too (change the dpi first, because it changes the pixels).
2. use Image / Mode to change to 8 bits / pixel (you should usually use 16 bpp for editing)
3. use File / Save As and change the file type to JPEG
If that produces a JPEG that looks different from the Save for Web command, then you can join the vast crowd who DON'T use Save for Web